Born in Darkness
by zero ideas
Summary: Touma was born in academy city knowing its darkness and raised in it he was an assassin a killer an esper unrivaled in the darkness that no one knew about and was alone but that changes (Harem and if you want a girl in the harem leave her name in the reviews no oc ) main pairing Touma and Mikoto (i am using Touma instead of Toma deal with it)
1. Chapter 1 Darkness

**hey everyone like i said on my blog i would make one of these and i might not update often because i haven't seen much of the series **

**i dont own a certain magical index**

Chapter 1 Darkness

There stood a boy with black spikey and dressed in a black hoodie and blue jeans was standing there in an abandoned building overlooking a city far more advanced than any other in the world the boy looked only 8 but in his eyes you see a fully grown man that has seen blood shed darkness and other dark things that no child should see.

He looked at the city one more time before walking into the building and walks down the stairs and creats a knife out of thin air with his left hand as he walks and then stops at a corner and waits then a man walking by the corner holding a gun comes

Then boy moves swiftly and stabs the man in the throat killing him silently.

The boy then places his right hand on the dead man and he evaporates into tiny particles leaving nothing

The boy continues down the stairs and stops at a railing and looks down to see hundreds of men working all armed with guns and taking packages around the place the packages were full of explosives

The boy then continued to walk until he was in another room the room was filled with weapons and explosives. Looking around with no interest the boy then activated one of the explosives then snapped his fingers on his right hand leaving an echoing snap then vanishing right at the exit of the building and taking out a pocky stick from his hoodie pocket and put it in his mouth and then pulled out a phone and dialed a number

"I did what you asked and the building is the one with the smoke coming out of it and you might want to get here quick because I think a fire started and no I am not putting it out I only applied for the job of helping you guys take the building." The boy then put away the phone and vanished again with the snap of his fingers of his right hand.

In a distant building the boy watched the building be taken over and anti-skill put out the fire and arresting the people in there.

"You know you could have just stopped everyone in there and not blow a hole in the building" a person behind the boy said.

"Well Ms. Yomikawa I could have done that and told you the direction and have your superiors ask you how you did it or blow a hole in the building and get you to make something else in the report and why are you here shouldn't you be arresting someone or investigating something" the boy said as he continued to look at the building

Aiho looked at the boy and sighed "I am my superiors want me to investigate an urban legend the urban legend revolves around a being called darkness a person born from the darkness of academy city and harvest its darkness to gain more power and knowing the darkness in academy city is something you are in you are after all the darkness" Aiho said as she looked at the boy

"What makes you think that and why that is an urban legend" he said not really caring

"It's not a legend because the legend state that he appears anywhere like a ghost and can vanish like a ghost and you know the darkness of the city like non other if something is going on in the city's dark side you always know before it happens and also you and the darkness are too similar to not notice you appear and disappear like a ghost and never leave a trail unless you do so on purpose and you where born in the darkness hell I don't even know your name" Aiho said in a matter of fact tone

"Well congrats you now know who the darkness is the only object that no one knows about on any level besides he can kill you if you so much as blink and know he was made in the darkness of this fair city" the boy said before vanishing leaving Aiho there thinking on what he said

That was the last time anyone saw the darkness and lived to tell the tale

8 years later

"So let me get this right Ruiko you want me to go and look at an urban legend in the anti-skill case files" Uiharu said in shock that her friend said

"Yes Uiharu I can feel it this legend has something to it and I want to know so please can you do it I would owe you big time" Ruiko said as she put up a her hand s in a begging gesture

Uiharu sighed "fine I will look what is the name of the legend you want me to look up" Uiharu asked pulling out a laptop from her bag

"Well I heard it's called Darkness a being born in the city's darkness and appears like a ghost and disappears like a ghost" Ruiko said

Uiharu then typed up darkness in the search area and found one file that stated that it had been last updated 8 years ago "Here it is Ruiko" she then clicked on it only for a password protection to pop up and at the top it stated file restricted

"See there is something on it" Ruiko said

"Okay just let me get pass the lock" Uiharu said then typed the access password in only to receive password denied "that's odd I can't in" Uiharu said then trying again

"It won't work it's a different password reserved for only those that were working on the case" a voice behind them said

They both turned around to see Aiho

"Ahio-san then could you help us then my friend just wants to look" Uiharu said

"Well the case file isn't much use it only gives you some info on his ability and small sittings nothing much the only thing that you can get real info on him is me." Aiho said as she sat down with them "there are only a few things I know and the most important of them all is his name and that is not in the case file"

"Well what is his name and what is he like and have you seen him" Ruiko said hoping to get info on the urban legend

"Well I can't tell you much on him besides all the rumors on him are true and he is about level 5 and probably the strongest out of them all and that was the last time I saw him and the last time I saw him was 8 years ago when he was 8 and helped anti-skill get rid of a terrorist group and his name is Touma Kamijou" Aiho said.

**hope you all like want a girl in the harem put her name in the reviews so ya see ya all later bye.**


	2. Chapter 2 he's back

**hey every one here is the next chapter and note some of the characters will be a bit out of character so ya **

**i dont own a certain magical index**

Chapter 2 he's back

"How the fuck does he does this." Gensei Kihara an elderly man said as he observed where a testing facility was supposed to be there now there was well there was nothing only an empty lot.

"I do not know sir the camera's around the area didn't catch anything" one of the guards there said to Gensei

In the distant a 16 year old boy looked over the scene and smiled at the scene

"You know that he can just use another facility Touma so why did you get rid of that facility when you knew they could always build another one or use another one" a women said behind the boy now named Touma.

The women had long black hair and black eyes and a slim figure, this person was Shutaura Sequenzia

"Well Shutaura I have my reasons for everything and each move has its own purpose and call Awaki we all need to talk" Touma said as he walked pass Shutaura

"Why do we have to have her here she is worthless to me and a danger" Shutaura said as she walked behind Touma down the stares

"Yes, to you and she is strong and reliable and loyal so don't hate on her too much even if you two would slit each other's throats when you have the chance" Touma said before vanishing leaving Shutaura there at the end of the stares

"That man is so confusing yet I can't help but love that about him" Shutaura said with a small smile she then pulled out her phone and dialed a number and waited

"What do you want" said a feline voice said

"The darkness wants you to come and meet up" Shutaura said

"Well if it's he then I will definitely come now where the location is" the voice said

"The usual place" Shutaura said then hanging up the phone "that bitch thinks she can take him well you have another thing coming Awaki"

In a different place

"Onee-sama you shouldn't be doing judgement's job" Kuroko said as she walked with Mikoto Mikasa the third strongest level five in the city and the rail gun.

"Well Kuroko then shouldn't judgment speed it up then" Mikoto said

"Onee-sama" Kuroko sighed then picked up her phone to see a message from Judgment "Onee-sama I have to go" she then left Mikoto there

Mikoto walked to the park and to the vending machine to hear "such misfortune" she turned to see a young man wearing a black jacket with black lining and Hawaiian tribal pattern in red on the sleaves and back had a normal yin-yang with the hood down and wearing black jeans looking at the vending machine.

"You lost your money to the machine" Mikoto asked

"ya I did" he said the boy had black spiky hair "the names Touma" said as he turned to Mikoto.

"Misaka Mikoto here let me help" Mikoto then gave kick to the machine brining two drinks down she then turned to look at Touma who was standing there reaching for a drink "I am surprise most people would be shocked at what I did" Mikoto said

"Well I know a girl that if you tick her off enough she would teleport you of the side of a skyscraper and at the last second teleport you to the ground safely and another girl that will blow you to bits if you so much as whispered the word miracle but she stopped after a certain incident" Touma said of handedly then taking a drink out of the can.

"Well you have some very interesting friends there Touma" Mikoto said as she took her drink

"You'll meet them now since they are here" Touma said

"Touma-kun!" Mikoto turned looked up at the air and saw a red headed girl wearing a jacket as a cape and had a bandaged chest coming down at Touma who side and whispered "such misfortune"

She had landed right on top of Touma hugging him

"Awaki can you please get off me" Touma said

"Nope" Awaki said cutely as she hugged Touma tighter

"You bitch get off him!" someone said behind Mikoto she turned to see Shutaura standing there with a black t-shirt and a black skirt

She then threw three shuriken made of a special metal at her which Awaki teleported away and then Shutaura tackled her to the ground and freeing Touma from Awaki's embrace

"Those are the two I was talking about" Touma said getting up and dusting himself "they are slightly crazy but you will get used to it if you get to know them"

Touma then walked over to the two them and pulled them off of each other

"Could you stop fighting each other and introduce yourself to Mikoto" Touma said as he looked at the two

"Well if it's for you Touma-kun then fine I am Musujime Awaki" Awaki said as she introduced herself to Mikoto

"My name is Sequenzia Shutaura nice to meet you" Shutaura said to Mikoto introducing her self

"Nice to meet you both" Mikoto said

"Now since we are introduced and all why don't we get going see ya later Mikoto" Touma said then walked off with Awaki and Shutaura following behind him

With Touma and the others

"You two do know that she was the rail gun right" Touma said

They both nodded in conformation and continued to walk into an old abandoned building

"Okay Shutaura earlier you asked me why I attacked that facility in particular well here is the answer" Touma said then pulled out a disk case holding a disk "that facility held the information on multiple projects that Gensei is planning and a project named the sisters project the copy of the Rail gun of academy city."

He then handed Shutaura the disk

"Now they have a plan of slaughtering over a thousand of these sisters, they may be clones but they are still living beings with emotions so we are going to stop this plan you two read up on the plan and we will meet up in a week at the same location and if you need me you will find me in my apartment" with that said Touma vanished

h**ope you liked and touma's power is something more powerful and to set of an explosion with explosives its not that hard its press of a button or a switch and also yes image breaker is still there and also he has another power bye **


	3. Chapter 3 magic and breaching

**hey everyone and thanks for the reviews and also i know my grammer is bad but hey i am doing these chapters at night so ya and also i am taking considerations to the girls you put hope you like **

**'thoughts'**

**"speaking"**

**i don't own a certain magical index **

Chapter 3 magic and breaching

The sun was rising for it was morning for Touma as he woke up. He then walked out get air and the first thing he saw was a nun lying on his balcony rail

He blinked twice then three times then he heard a growling sound

"Hungry" the nun spoke she was still unmoving

"What the fuck" was all Touma could say as he looked at the nun thewn it clicked in his head he then picked up the nun and took her into his apartment

'let's see a nun is in my apartment and is hungry I have 2 choices think his is a dream and try to wake up or go along with it and get answers *sigh* as much as the first option seems so tempting but the last option would be the best course of action' Touma then put the nun down on the ground and cooked up some rice and eggs nothing much and nothing special.

Once he was done with it he placed the plate of food on the table and waited

The wait was only for a few seconds; in a flash the nun was eating the plate of food in a flash.

Once the nun was done Touma sat down and looked at her and sighed "so can you tell me your name since I fed you"

"My name is Index and thank you for feeding me" Index said satisfied from the food.

"Okay next question why were you on the railing" Touma asked

"I was running away from magicians that wanted to take the 103,000 grimoires inside of me" Index said seriously which didn't quite look serious at all.

"Wait you are saying that magic exist in this world and that some are chaseing you and you have 103,000 books in your head, you do know that this is very hard to believe" Touma said trying to process on what he had heard and somewhat processing it.

Index nodded in confirmation

"Well that explains some of the weird shit I have seen" Touma said as he remembered seeing a lady summon a rock monster and just drew on the walls and eyes would pop out. To simply put it they fought he won end of story.

"Sigh you best be staying here then if magicians are coming after you" Touma said as he got up and was about to leave the room and prepare for his activity for tonight.

"Wait then you would be in danger of them" Index said worried for Touma

"Relax I have fought a magician before their magic won't work on me" Touma said as he continued leaving a confused Index

In the room with Touma he looked up to see a map on the wall and a building was circled. He then walked to a table and attached a gun Hollister to his hip and placed a pistol in it and a few clips for the gun 'Better safe than sorry' he thought as he then put up his hood

"If you get hungry there is some food in the fridge just heat it up" Touma said as he walked out the door leaving index

Later that night

In a facility out of the area of academy city there in the darkness was Touma who then walked through the facility not caring for a thing and stopped at one room.

"Here we are" Touma said as he walked into a room sealed off from the rest.

The room had one main computer and the rest was a window to some chambers. Touma then walked to the computer and activated it and looked through it to find what he was looking for.

The level 6 shift

"Let's see they are using accelerator and killing 2000 clones of rail guns" Touma said as he skimmed through the files and how cruel the experiment was.

He then herd the door open he then turned around to see Misaka Mikoto the real one

"Um hi Mikoto" Touma said as he turned fully around and looked at her.

"What are you doing here Touma and are you part of this?" Mikoto asked as she sparked some electricity.

"Well you could say I am involved but not on the side that clones you and kills them" Touma said as he raised his hands in a surrendering gesture.

"What will make me believe you?" Mikoto asked threateningly not letting her guard down

"Well I have nothing to prove it but I promise that I am not involved in the plan and look what would I gain if I helped them achieve this there would just be another insane sicko path in the city and there are already a lot of them." Touma said trying to prove that he was not part of the experiment but only failing "such misfortune, okay what if I told you that this could all be stopped"

This peeked Mikoto's interest but it didn't make her drop her guard.

"How so" she asked

"Well you know that the one doing the experiment is accelerator right so why don't we beat him it simple as that" Touma said as he walked closer Mikoto "and also I am not your enemy I am your ally just ask for help and I will assist you"

Mikoto let her guard down a little and looked at Touma "how did you get in" she asked

"Well I destroyed the door and destroyed everything in my way" Touma said sheepishly.

"Okay now tell me if you knew about the project why haven't you stopped it" Mikoto asked

"Mikoto you should know that they would just restart I need to get info on the leader of this project and eliminate him after all you know it's no use to take one problem out and not take the root out first" Touma said as he walked up to Mikoto "by the way you look nice in civilian clothes you should wear them more often" Touma said then walked past her vanishing leaving a blushing Mikoto

"Idiot" she said faintly and noticed the paper I her hand

_Don't face him alone and if you need help go to the place we first met_

_Sincerely-_

_Touma Kamijou _

Mikoto smiled then got to work.

**hope you like if you want a girl in the harem leave her name and also remember touma has another ability and image breaker is still there just modified to my thoughts so bye. **


End file.
